Dissection of intercellular communication using the transcriptome-based framework ICELLNET

This repository hosts the source code corresponding to the method described in Noël, F., Massenet-Regad, L., Carmi-Levy, I. et al. to infer intercellular communication networks and dissect intercellular communication between multiples cell types based on their transcriptomic profiles.

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ICELLNET key features:

• Contains a manually curated ligand-receptor interactions database: curated exclusively from human studies, ICELLNET database takes into account the multiple subunits of ligand and receptor complexes (more than 1600 interactions)
• Versatile tool applicable on a wide range of transcriptomic technologies (microarray, bulk RNAseq, scRNAseq, spatial transcriptomics)
• Several visualization modes of cell-cell communication analysis results

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New on ICELLNET v2 - corresponding paper link

• New structure and extension of ICELLNET database up to 1669 interactions.
• Possibility to ICELLNET analysis using other databases such as CellPhoneDB as input.
• Updates of several functions to match the new structure of ICELLNET database.

Additional details on updates and previous versions can be found here.

Remark: ICELLNET v2.0.0 requires R version < 4.1. For latest R versions (> 4.1.x), please use ICELLNET v2.2.x.

Information related to ICELLNET and tutorials

• Detailed documentation
• ICELLNET analysis on scRNAseq data: Tutorial
• ICELLNET analysis on sorted cell-population transcriptomic data:
  • Script: analyze cell-cell communication between different cell populations from the same sample
  • Tutorial: infer cell-cell communication from the transcriptome of a single cell type of interest with the Primary Cell Atlas (Database of reference transcriptome of 33 cell types).

Installation

Installation of dependencies:

install.packages(c("devtools", "jetset", "readxl", "psych", "GGally", "gplots", "ggplot2", "RColorBrewer", "data.table", "grid", "gridExtra", "ggthemes", "scales","rlist")) ##Installs devtools and the icellnet CRAN dependancies

if (!requireNamespace("BiocManager", quietly = TRUE)) # Installs icellnet Bioconductor dependancies 
    install.packages("BiocManager")
BiocManager::install(c("BiocGenerics", "org.Hs.eg.db", "hgu133plus2.db", "annotate"))

Installation of ICELLNET package:

library(devtools)
install_github("soumelis-lab/ICELLNET",ref="master", subdir="icellnet")

Once all the dependencies are downloaded and loaded, you can load the ‘icellnet’ package.

Citation

If you use our human curated ligand-receptor interaction database or the ICELLNET method, please cite our papers:

Noël, F., Massenet-Regad, L., Carmi-Levy, I. et al. Dissection of intercellular communication using the transcriptome-based framework ICELLNET. Nat Commun 12, 1089 (2021). https://doi.org/10.1038/s41467-021-21244-x link

Massenet-Regad L, Soumelis V. ICELLNET v2: a versatile method for cell-cell communication analysis from human transcriptomic data. Bioinformatics. 2024 Mar 4;40(3):btae089. doi: 10.1093/bioinformatics/btae089. PMID: 38490248. link